Archive for March, 2011

Would you prefer to have sex with males or females? It’s such a simple question, but a loaded one. Biologically, we know very little about what goes on behind such sexual choices, in humans or other animals. Socially, it’s a question that can provoke fierce debate, social stigma, and psychological anxiety. Into this minefield steps a new study from Yan Liu and Yun’ai Jiang at Beijing’s National Institute of Biological Sciences.

Here’s the simple version. They found that male mice lose their normal preference for female mice if they have low levels of serotonin – a hormone that carries signals in the brain. Instead, they try to mate with individuals of both sexes, in equal measure. Inject them with more serotonin, and you can restore their preference for females. The obvious conclusion is that serotonin affects the sexual preferences of mice. The obvious question is whether it also affects the sexual preferences of humans. And, as is often the case, it’s a little more complicated than that.

Serotonin is no stranger to sexual behaviour. With lots of serotonin around, male mice lose interest in sex. Their libidos fall, they lose erections and they fail to ejaculate. If you kill the neurons that respond to serotonin, you can reverse these effects and restore the rodents’ sex drives. The same thing applies to humans. This is why people who take SSRIs – antidepressant drugs that raise levels of serotonin – often face a variety of sexual problems. Liu and Jiang wanted to extend this work to see if serotonin can also influence an animal’s choice of sexual partner.

This monstrous fish is a tambaqui, a close relative of the piranha. Fortunately, it doesn’t share its cousin’s flesh-eating lifestyle. Instead, the 30-kilogram tambaqui (or pacu) is a vegetarian. It swims through the flooded forests of the Amazon, eating fruits that drop from the overhanging trees. In doing so, it acts as an vehicle for the Amazon’s seeds, carrying them to distant parts of the jungle within its gut.

This is a role that we normally associate with birds or monkeys, but Jill Anderson from Cornell University has found that the tambaqui is a champion seed carrier. It can spread seeds over several kilometres, further than almost any other fruit-eating animal on record.

In 1958, a young scientist called Stanley Miller electrified a mixture of simple gases, designed to mimic the atmosphere of our primordial lifeless planet. It was a sequel to one of the most evocative experiments in history, one that Miller himself had carried five years earlier. But for some reason, he never finished his follow-up. He dutifully collected his samples and stored them in vials but, whether for ill health or dissatisfaction, he never analysed them.

The vials languished in obscurity, sitting unopened in a cardboard box in Miller’s office. But possessed by the meticulousness of a scientist, he never threw them away. In 1999, the vials changed owners. Miller had suffered a stroke and bequeathed his old equipment, archives and notebooks to Jeffrey Bada, one of his former students. Bada only twigged to the historical treasures that he had inherited in 2007. “Inside, were all these tiny glass vials carefully labeled, with page numbers referring Stanley’s laboratory notes. I was dumbstruck. We were looking at history,” he said in a New York Times interview.

By then, Miller was completely incapacitated. He died of heart failure shortly after, but his legacy continues. Bada’s own student Eric Parker has finally analysed Miller’s samples using modern technology and published the results, completing an experiment that began 53 years earlier.

This post was originally published on 7 April 2010. I am reposting it in honour of the release of Open Laboratory 2010, which has just come on sale. It’s an anthology of great blog posts from last year, including this one.

Japanese people have special tools that let them get more out of eating sushi than Americans can. They are probably raised with these utensils from an early age and each person wields millions of them. By now, you’ve probably worked out that I’m not talking about chopsticks.

The tools in question are genes that can break down some of the complex carbohydrate molecules in seaweed, one of the main ingredients in sushi. The genes are wielded by the hordes of bacteria lurking in the guts of every Japanese person, but not by those in American intestines. And most amazingly of all, this genetic cutlery set is a loan. Some gut bacteria have borrowed their seaweed-digesting genes from other microbes living in the coastal oceans. This is the story of how these genes emigrated from the sea into the bowels of Japanese people.

Within each of our bowels, there are around a hundred trillion microbes, whose cells outnumber our own by ten to one. This ‘gut microbiome’ acts like an extra organ, helping us to digest molecules in our food that we couldn’t break down ourselves. These include the large carbohydrate molecules found in the plants we eat. But marine algae – seaweeds – contain special sulphur-rich carbohydrates that aren’t found on land. Breaking these down is a tough challenge for our partners-in-digestion. The genes and enzymes that they normally use aren’t up to the task.

Fortunately, bacteria aren’t just limited to the genes that they inherit from their ancestors. Individuals can swap genes as easily as we humans trade money or gifts. This ‘horizontal gene transfer’ means that bacteria have an entire kingdom of genes, ripe for the borrowing. All they need to do is sidle up to the right donor. And in the world’s oceans, one such donor exists – a seagoing bacterium calledZobellia galactanivorans.

Zobellia is a seaweed-eater. It lives on, and digests, several species including those used to make nori. Nori is an extremely common ingredient in Japanese cuisine, used to garnish dishes and wrap sushi. And when hungry diners wolfed down morsels of these algae, some of them also swallowed marine bacteria. Suddenly, this exotic species was thrust among our own gut residents. As the unlikely partners mingled, they traded genes, including those that allow them to break down the carbohydrates of their marine meals. The gut bacteria suddenly gained the ability to exploit an extra source of energy and those that retained their genetic loans prospered.

In Israel’s Khai Bar Reserve, a pair of brown-necked ravens has a problem. They’re after the tasty contents of ostrich eggs and there are plenty to go around. The eggs – the largest of any bird – would provide a nutritious meal but they’re so thick that even a pair of ravens can’t puncture them. But they don’t need to. The ravens know that the desert is also home to a master egg-cracker – the Egyptian vulture. All they have to do is wait, and they can rob the robber.

Shai Kabesa from Ben Gurion University first noticed the ravens at work in 2008. Together with Reuven Yosef, she pieced together their strategy in the following years.

The Khai Bar Reserve has no native ostriches – they were hunted to extinction in the area during the 1940s. There is, however, a thriving conservation project that’s breeding the birds in the hope of reintroducing them. Ostriches lay their eggs in a single nest. The dominant female goes first, laying around 15 to 20. Her subordinates follow with 3 to 4 of their own. However, the top pair of ostriches can only incubate around a dozen eggs effectively, and they roll the rest away from the nest. This creates a ring of nutritious treats for any bird skilful enough to break into the eggs.

The Egyptian vulture does so with a special technique – it uses a tool, and is one of the few birdstodo so. It picks up rounded stones in its beak and uses them to hammer the egg shells until they crack. Even ostrich eggs eventually give way. But the vultures don’t always get to enjoy the fruits of their labours. Yosef found that on at least three occasions, a pair of ravens, watching nearby but hidden behind a bush, quickly flew in and drove the vultures away.

“Sh*t!” my dad says. Geoblogger Evelyn Mervine interviews her dad (a nuclear engineer) on Japan’s current situation. A great example of the ability of the web to empower people who might not otherwise have had a voice. This is also worth noting for the crowdsourced transcription effort!

Two pieces at the Economist: one covering the recovery process, attempts to cope with dwindling food, how the economy will respond, and the national’s cultural reactions; and another looking at the effects on the energy industry and the country’s position at a crossroads in history.

“Hours after the first shock waves hit, two of the largest crime groups went into action, opening their offices to those stranded in Tokyo, and shipping food, water, and blankets to the devastated areas…” Even the Yakuza are helping out. Awesome story by Jake Adelstein at the Daily Beast

Possibly my favourite thing of the year – Craig Venter got a cease and desist letter from the Joyce estate after including a line from one of Joyce’s poems in the genome of his synthetic organism. He also messed up a Feynman quote. Maybe version 2.0 can have a retraction and correction in it?

Jonathan Eisen finds something… weird. Is it a fourth domain of life or just some freaky viruses? Or both? New Scientist has an easy take, and Carl Zimmer has a masterful piece that provides some context and includes a guest appearance from me and my “Yong-o-matic Horizontal Gene Transfer Injector”. But surely for the most thorough (but hardest) version, you should go to the man himself.

I was going to do an April Fools’ post on the Journal of Cosmology but I can’t outdo their actual staff. NASA’s Chief Scientist is a Grand Inquisitors, journalists are on their payroll, there’s a big cover-up, none of the critics of Hoover’s paper (on bacteria’ fossils in meteorites) are “legitimate scientists”, and so on. Meanwhile, Chandra Wickramasinghe speaks about his sacking by Cardiff University

“I do not want to resort to hyperbole, but it feels like a whole generation of would-be scientists is being snubbed” Nathan Ley on what it’s like to apply for a studentship in the UK just as the government’s austerity measures start to bite

The power of lonely – what we do better without other people around. Other than using the toilet.

When did Europeans first harness fire? Later than thought, apparently. And how does Richard Wrangham react to an idea that contradicts his hypothesis that cooking helped drive human intelligence? Rather charmingly, it turns out.

“Oh, that internet. It has not a single citation and it is positively full of blackguards and scoundrels.” I’m paraphrasing. Read the actual response from McDermott & Rosen on the charge of ignoring the post-publication peer review of arsenic life.

I like to think of myself as an “Apatosaurus denialist.” Brian Switek eulogises Brontosaurus

“Both science and spirituality came from space.” “We have to conclude that the second law has in fact been violated here”. Applied Mathematical Letters has all the best retracted papers.

I finally downloaded my recordings from the ScienceOnline 2011 conference that I attended back in January. Here are a couple of sessions for your listening pleasure. These were recorded using my Livescribe pen so the audio is passable if not brilliant.

The first is the Death to Obfuscation workshop, featuring Carl Zimmer and myself. It’s on writing about science for a broad audience, who isn’t obliged to read your stuff. We consider basic elements and pitfalls that writers need to consider, from the level of individual words and sentences, to paragraphs and pieces. The audio’s a bit tinny because the pen was near a projector and the audience questions are a bit muffled, but you can hear pretty much everything that Carl and I are saying. I’ve cut out a bit near the end with a written exercise because the sound of 70 people writing for 5 minutes isn’t particularly gripping.

Few groups of animals hold such special significance for us as the primates – the apes, monkeys, lemurs and more. This is the group that we are a part of. Its members are familiar and charismatic, but our evolutionary history is tangled and occasionally controversial.

Now, Polina Perelman has provided the most comprehensive view of the primate family tree to date. Her team sequenced genes from over 186 species, representing 90% of all the genera that we know of. Her tree confirms some past ideas about primate evolution and clarifies other controversies. It’s a story of island conquests, shrinking bodies, tangled branches and ancient relics. This slide show tells that story.

Video game players are used to replaying history. They can load up any saved game and start afresh, sometimes making different choices that lead to alternative endings. Life, sadly, is no game and it’s far more difficult to reload and start again… difficult, but not impossible. In a laboratory in Michigan State University, Richard Lenski repeatedly replays evolution from saved files.

Lenski’s aptly named “long-term evolution experiment” is the longest-running in history, and one of the most important. It looks deceptively simple – just twelve gently shaking flasks of sugary solution, each containing a strain of the gut bacterium Escherichia coli. Lenski bred the dozen strains from a common ancestor in 1998. Every day since then, his team has transferred one per cent of the cells into a fresh flask to grow anew. Last month, the bacteria passed their 50,000th generation.

Every 500 generations, the team takes a sample from each of the dozen strains and freezes them. These stocks are the experiment’s “fossil record” – its living save-files. By thawing them out and growing them afresh, the team can compare their fates to that of the original dozen. As the late Stephen Jay Gould once said, they can “replay life’s tape”.

In natural history films, lionesses are usually portrayed as the hunters of the pride, while male lions mope around under shady trees. But males are no layabouts – they’re effective killers in their own right, particularly when they target larger prey like elephants and buffalo. Aside from humans, lions are the only predators powerful enough to kill an elephant. The males, being 50% heavier than the females, are especially suited to the task. It typically takes seven lionesses to kill an elephant, but just two males could do the same.

Even a single male can overpower a young elephant. Between 1994 and 1997, Dereck Joubert found that the lions of Botswana’s Chobe National Park were getting better and better at hunting elephants. He wrote: “In one notable case, a single male lion ran at nearly full speed into the side of a 6-year-old male calf with sufficient force to collapse the elephant on its side.”

Male lions clearly pose a great threat, and older elephants know it. Karen McComb from the University of Sussex has found that older matriarchs – the females who lead elephant herds – are more aware of the threat posed by male lions. If they hear recordings of male roars, they’re more likely to usher their herd into a defensive formation. Their experience and leadership could save their followers’ lives. “Family units led by older matriarchs are going to be in a position to make better decisions about predatory threats, which is likely to enhance the fitness of individuals within the group,” says McComb.